The Master Plan
by John Hawkman
Summary: Serenity takes on an enthusiasic passenger with a love for transport ships, unaware that the man's old enemy is lurking in the shadows...
1. Chapter 1

Mal Reynolds stood on top of his ship, holding a golf club.

"…and then she makes it sound like I did it on purpose," Wash said

"Interesting…" Mal took a swing, "but I still think she has a right to be mad at you."

"Why?" Wash groaned, "Why is everyone taking her side?"

"Do you really expect me to take your side in a story that began with you throwing a brick at your wife?" Mal pointed out

"Well…not immediately!" Wash admitted

He swung his club, sending the ball flying. Shepherd Book stepped onto the strip of putting green, and took his swing.

"I don't know, hearing Wash's version does make it sound like Zoe was asking for it," Jayne admitted

Jayne flipped a couple of burgers on the grill; Simon unbuttoned his shirt, and laid down on his lounger.

"Yeah, but if I asked you to stab me, would you do it?" Simon asked, applying sun block

"You wouldn't have to ask," Jayne muttered

In the kitchen…

"…and then he accused me of putting thumbtacks in his cereal!" Zoe explained

Inara put down the scissors she was using to cut River's hair.

"Did you?" Inara asked

"Yeah, but the point is he accused me of it!"

"Why did you put them in his cereal?" Kaylee asked

"That's not the point," Inara reminded, "it's a trust issue."

"So you don't think it was going too far?" Zoe asked

"No, I think you went too far when you said you'd forgive him if he ate a light bulb," Inara said

"I don't think she expected him to do it," Kaylee said

On the roof…

"So she didn't know you ate her engagement ring?" Jayne asked

"I think it was pretty obvious! I said I dropped it in the wedding cake batter, she could have figured out the rest !"

"Is that why you ate a light bulb?" Simon asked

"No, that was because…"

Kitchen…

"I don't see how the term 'frigid-wolverine-bitch' can be said politely at a family dinner!" Zoe continued

"Then why'd you say it?" Kaylee asked

"I have my reasons!"

Roof…

"I think a man should be allowed to hit his wife once," Jayne confessed

"Thank you!" Wash said

"But when she can hit back it's common sense not to."

Kitchen…

"Kissing another woman is one thing, but another man?" Zoe asked

Roof…

"Just how terrified of her are you?" Book asked

"I'm not afraid of her, I just don't like being alone with her in the dark!" Wash yelled

Kitchen…

"I was young and needed the money!" Zoe exclaimed

"But that video was dated from last month?" Kaylee was confused

"Are you saying that I'm old?" Zoe growled

Roof…

"…well I'm sorry if a religion based on a classic earth film sounds impossible, but five `generations can't be wrong…"

"Excuse me, am I interrupting something?"

The four guys turned around, and saw some guy in a dark blue suit with a brown overcoat standing by the starboard ladder. He was smiling like no backwater-man would.

"Sorry, don't mean to intrude," the guy reached into his coat pocket, and took out a metal tube, "I'm looking for a friend of mine. Well, not a friend…"

Jayne stood up, and took out his Ruger Redhawk gun.

"Look buddy, if you're one of Badger's friends, we're not interested," Jayne growled

"Badger…" the man muttered, "wait! Is this…"

The man tapped the ship with his feet. Mal could see the guy was wearing sneakers; obviously not a bounty hunter.

"Oh! This is a transport ship!" he was grinning wider than Mal had ever seen, "I love a good transport ship!"

The man started running around Serenity's crew.

"Firefly class! Excellent, this is just like an episode of Top Gear! And your crew! Gun hand, Doctor, Shepherd, Captain, pilot! The complete set!"

"Uh, excuse me Mr. Happy Fruity-Oaty man, as much as I like you coming on the roof of my ship uninvited, I just have one question," Mal said

"Anything," the man said

"Who the h-ll are you?"

"I'm the Doctor," he said

Jayne tightened his grip on his gun.

"And I'm not an Alliance agent, if that's what you're thinking," The Doctor said quickly

Jayne placed the gun back in the holster.

"Well, if you're not an Alliance agent, then who are you?" Wash asked

"Oh, just a traveler," The Doctor replied, "I thought I tracked my mate to here, but I guess I was wrong."

The Doctor pointed his metal tube into the sky, and waved it around. It made a peculiar sound, like a metallic whistling.

"Nope. Coordinates were correct. Unless someone was using a hair dryer?"

"A what-dryer?" Jayne asked

"Are you grilling?" The Doctor asked, "because I am starving. Just flew my ship silent-running through the tenth Sontaran Battle fleet; three days, and I couldn't even get up to go to the kitchens."

"Here," Jayne handed him a hot dog, hoping it would shut him up

"Thanks," The Doctor took a bite out of it, "so, taking a break from work? Skiving off while the boss is away?"

"It's not really a break, we just can't get hired," Mal explained

"Is that so? This time in history should be filled with your line of work."

"Well…it's complicated," Mal said, "crewmember of ours has the Alliance after him."

"Uh huh…I didn't get your name."

"Mal Reynolds," he said, "that's Wash, Jayne, Book, and Dr. Simon Tam."

The Doctor's eyes widened.

"Simon Tam!" he grinned "As in River Tam's brother?"

Jayne cautiously reached for his gun.

"You seem to know an awful lot about her," Simon said carefully

"How could I not know River Tam?" the Doctor grinned, "Scientist, dancer, fantastic writer!"

Mal also reached for his gun, Book picked up his nine iron threateningly.

"Is she here? Could I meet her?" The Doctor grinned

Simon got up from his lounger, and picked up a frozen steak, planning to clobber the Doctor with it.

"No! You know what, I think I have a job for you," The Doctor said

Mal grabbed the steak from Simon, and motioned for Jayne and Book to put down their weapons.

"Really?" Mal asked

The girls joined the guys moments later; they caught them in the middle of drinking beer and laughing.

"…and then I told her, she'd look like a sheep on its hind legs!" Mal said

They all laughed.

"You're in a good mood," Inara commented

"Why shouldn't I be?" Mal asked, "this Doctor just offered us a wad of cash to transport something for him."

"Really? How much?" Zoe asked

"Enough for us to take a couple of weeks off," Mal said

"Can I get that compression coil?" Kaylee was excited

"Sure," Mal replied, "you can have ten."

"Wait, who is this guy?" Zoe interrupted

"He's the Doctor," Wash said

"Doctor who?" Zoe asked

Later that night…

The guys stood around a fire in the cargo bay, roasting marshmallows. Wash and Jayne wheeled the Doctor's cargo in, a large blue crate with 'Police Box' written on it.

"Is this it?" groaned Wash

"Yeah," the Doctor said, "hold on, I want to get something from it."

The Doctor disappeared inside his box. There was some cluttering about, and two minutes later he emerged holding a wooden guitar.

"You play?" Mal grinned

"A bit,"

The Doctor sat down on the bench next to Mal.

"This one's for all you ladies out there," the Doctor spoke with a mock country accent, "take my love, take my land, take me where I cannot stand…"

The girls had gone out for the night, going swimming in a nearby river. After a few shots of tequila, an innocent swim had become a skinny dip.

"Inara, you have a perfect body," Zoe complemented

"Thank you Zoe, that's very kind," Inara replied

"That's why I hate you."

Zoe jumped at Inara, dunking her head underwater. River turned to Kaylee, and shoved her underwater. Kaylee came up, desperate for air.

"Why did you do that?" Kaylee gasped

"You were going to do the same to me," River replied

"Excuse me, ladies," came a man's voice

The four girls looked up to see a man in a black Mao suit; he had a peculiar face: gray at the temples, slicked-back black hair and goatee, with an expression that made Jayne's 'I'll be in my bunk' look like Mary Poppins 'a spoonful of sugar makes the medicine go down'. The girl's hands shot up, covering their bare chests.

"Who are you?" Zoe demanded, "what do you want?"

"My name is The Master," the man grinned, "and what else would I want with four naked and wet women?"

Zoe leapt up and grabbed her sawn-off shotgun; The Master saw her, reached into his jacket, and took out a brass tube with a blinking orange light at the end and a chain at the other end leading to the man's wrist. He turned a dial on the side, and fired an electric blast at Zoe's hand. She dropped the gun in the water.

"Laser screwdriver, mark II," The Master said proudly

"Look, mister, I'll make you a deal," Zoe said, "let these girls go, and you can do whatever you want with me."

"I'm well above raping prairie-back-water-roughneck maiden," The Master replied gruffly, "this is what I want to do…"

He held up his laser screwdriver, and twisted a couple of the dials. Before the girls could get away, a bright red light blared out at them, and they were in a trance.

"You are under my command…" The Master said, with a deep voice

"We are under your command…" the girls repeated

The Master gave them his instructions, and then began to walk away. He only took a few steps, and then felt something soft under his foot. He switched on the laser screwdriver's flashlight mode, and saw that it was a pile of the girl's clothes. The Master grinned evilly.

"I may be above rape, but I'm never too old from for childish pranks."

Carefully, he turned his laser screwdriver to another setting; a blast of fire shot out from the red tip; Zoe's leather vest and khakis went up in flames; Inara's silk gown was singed beyond recognition; Kaylee's floral design chic was burnt to a crisp; River's loose dress and lycra shorts were destroyed.

"Ahahahaha!" The Master exclaimed, running away


	2. Chapter 2

Chapter 2

Please review (otherwise in Chapter Three there's going to be slash, and I don't mean the cool Inara/Kaylee or River/Jayne stuff…)

/

/

The next morning…

/

It was time for take-off. Most of the crew sat in the lounge area, buckled into their seats, except for Mal, Wash, and The Doctor, who were in the cockpit. Wash sat in his seat, the Doctor and Mal were in fold-down seats behind him.

"Absolutely fantastic," The Doctor grinned, slipping on his 3D glasses

"I've never seen a man so happy to be on a cargo flight," Mal confessed, "there's something strange about you, Doctor that I just can't put my finger on."

The Doctor was about to reply, but then he reached into his jacket, and took out his metal tube. It was whistling again.

"And what exactly is that?" Book asked

"It's a Gallifreyan multi-functional radar silent laser-tracker lock picking instrument with a quantum compression module and a custom handgrip."

"Huh?" Mal asked

"Sonic screwdriver," the Doctor simplified, "it picked up something for a moment. Never mind."

"OK…" Wash turned around to his controls, "Guidance systems in place. Launching in five, four, three, two, one…"

"Allons-y!" The Doctor pointed out to space

Wash slid the inertia brake off, and the ship took off. The twin side engines exerted all their force, and lifted the ship off. The Doctor's grin factor increased. They shook violently, but Wash knew it was normal.

"Activating firelight," Wash continued

The rear engine kicked in, allowing the ship to ascend. They rocketed through the skies, breaking atmo in under a minute…

/

"Well Doctor, I'm setting auto pilot," Wash said, "the exciting part is over."

"Oh, far from it," The Doctor grinned, "we're in the black now! Floating through space, the most beautiful vastness of nothingness in existence! I feel like a kid on Christmas!"

"I'm glad to see your enthusiasm, Doctor," Mal said, "it's a welcome change for a passenger, a lot better than the usual 'what was that are we going to die?'."

"Thank you," The Doctor replied, "Now, how about you join me for a drink?"

The Doctor reached into his overcoat, and took out a liter bottle of coke.

"Where did you get that?" Wash gasped

"Well, it started out when I was meeting a Judoon captain on the moon at a bar called Zoon…"

/

The Doctor continued talking whilst Wash and Mal escorted him to the kitchen.

"…and then I said 'roh moh shoh coh loh toh doh moh coh'," The Doctor replied

The Doctor laughed at his own joke; Mal joined and, and signaled to Wash to do the same. At the rate this guy was paying, Mal would have laughed at a 'dead browncoat' joke…well, he wouldn't have killed him for it.

"Sir, can we get dressed now?" Zoe asked

Zoe, Kaylee, Inara, and River stood in the kitchen wearing only black robes; they had woken up hung-over and naked by their campsite, and didn't have time to change before launch.

"OK, but be back soon, The Doctor's got a treat for us," Mal said

/

The girls left to get dressed; but as soon as they were out of sight, they changed directions. Kaylee walked to the engine room with Zoe, and they began to perform some alterations. River and Inara went to the flight deck and altered the navigation equipment. They had no idea what they were doing, they were under hypnosis.

/

"…and one for you," The Doctor poured Jayne a glass

"So this stuff has zero percent alcohol, ninety percent sugar, and a flavor from some nut in a long gone earth world," Jayne said, "and you want me to drink it?"

"Try it, you'll like it," Mal said

Jayne tried it, and did like it.

/

Two hours later…

/

A warning light flashed on the Wash's watch; it was a warning from Serenity he had built to detect Reavers; it could detect unshielded radiation in ships and excess exhausts. Wash checked it out; they were on a collision course to a Reaver gathering.

"No, no, no!" Wash exclaimed, "How could this have happened?"

Desperately, Wash tried to disengage the auto pilot, but nothing worked. He couldn't even switch off the engines, or call for help.

"Captain!" Wash yelled

At once, everyone was on the bridge, trying to get things to work.

"Worst case scenario, we shut off the engines and call for help," Mal said

"Tried it," Wash said, "doesn't work."

"Um, these Reavers," The Doctor said, "remind me, who are they?"

"They're space savages," Zoe said, "if we go pass through their territory and they capture our ship, they'll screw us to death and eat our flesh, in that order if we're lucky"

"I see."

The Doctor took out his sonic screwdriver, and aimed it at the controls.

"Deadlocked," The Doctor muttered, "that's weird. Deadlock seals aren't found in this part of the galaxy. Not for three hundred years."

Mal ignored the comment.

"So you can't fix it?" he asked

"I'm afraid not…"

"What if they don't detect any life?" The Doctor proposed, "what if there's no one on board?"

"Then they'd let the ship drift by, but we can't fake it to their scanners."

"I think I have just the thing."

/

Everyone followed The Doctor downstairs; they didn't have any other plans. They watched him climb into the blue box of his.

"Come on," The Doctor said, "get inside!"

"Late quantum state phenomenon," River said, "Gallifreyan. Only way to fit thirteen million Daleks in one Genesis Ark."

"Doctor, quit fooling around," Mal said, "you can't…"

Mal opened up the blue box, and gasped. Inside, there was an entire room, much bigger than Serenity's cargo bay. It was bronze on the inside, with coral-like support structures holding up the hexagon-paneled walls. The Doctor stood next to a green glowing column in the center of the room, which was surrounded by a tan-console that had an eerie green glow.

"How…?" Mal began

"Simple trans-dimensional engineering," The Doctor tossed his sonic screwdriver in the air, "now, do you want to get the rest of your crew in here?"

/

Everyone came inside, all equally amazed and shocked.

"So we hide in here until the Reavers pass us by?" Jayne asked

"Well, we could," The Doctor said, "or I could just travel forward in time until we've passed the Reavers?"

"Doctor, be serious," Mal grinned, "a warehouse in a box is one thing, but time travel? Come on…"

"OK," The Doctor nodded

He flipped a couple of switches on his console, and hit one with a hammer. Suddenly, the column in the middle of the room started to ascend and descend, making a strange whirring sound.

"What's going on?" Jayne asked

"Oh, nothing," The Doctor said, flicking a few switches

The column stopped moving.

"Wash, take a look outside, would you?" The Doctor asked

Wash reluctantly opened the door; to his surprise, there was a Tyrannosaurus Rex standing outside in a humid jungle. He closed the door.

"Yep, definitely a time machine," Wash muttered

/

Very quickly, the Doctor took them back to their ship, only later; there were a few Reaver spikes in the hull, but no serious damage.

"You guys are now twelve hours out of sync with regular time," The Doctor grinned, "Molto bene."

"Doctor, there's one thing I don't understand," Shepherd Book said, "if you have a machine that can travel anywhere through time and space, then why go on our ship?"

"Well, it's like with visiting Paris. There are tall buildings back home you could be walking up, but it's more fun to go up the Eiffel tower."

No one knew what an Eiffel tower was, but they didn't say it.

"OK, Doctor," Mal said "I'd better call the port authorities, tell them we'll be early,"

"I've got to set a new course," Wash said

"Can I watch?" Doctor asked

"Of course."

/

"Port Base, this is Malcolm Reynolds," Mal said

No reply.

"Port Base, come in."

Still nothing. Then there was a faint blip.

"Wash, can you boost that signal?"

"Hold on…"

Wash flicked a switch, and the blip became louder.

"Reyn…Reyn…Reyn…" the same syllable kept repeating

"No…" The Doctor said, "Not now…"

Wash checked some other devices; the space-sonar was on a loop, so was the wave-network, and even the verse-clock.

"Doctor, could your machine have done this?" Mal asked

"I might have landed in a time trap," The Doctor theorized, "it's a fixed point in time that repeats itself continuously so someone can't escape. Like a temporal speed trap."

"Why would one of those be on Serenity?" Kaylee asked

"Only one reason I could think of. Remember that friend I told you I was looking for?"

Suddenly, a screen flickered to life, showing The Master.

"Doctor…" he grinned

"Master…" The Doctor breathed, "What are you doing here?"

"I'm planning to usurp control of the Alliance of Planets," The Master replied, "And I can't do it with you interfering."

He held up his laser screwdriver at the screen, and suddenly, he was in the cockpit.

"Wait a minute, this is wrong," The Doctor said, "that incarnation of you hasn't met this incarnation of me yet!"

"Au contraire, Doctor," The Master grinned

He held up his laser screwdriver, and flicked a dial; he switched from the form of a classic villain to a less impressive thirty-something guy with bleached-blond hair in a cheap suit. The only thing that remained was the sleazy grin.

"Regeneration cycler," The Master grinned, "allows me to move within time completely undetected."

"What's your plan, Master?" The Doctor asked

"Doctor, do you really expect me to tell you my plan if there was any chance you could stop it? I did it thirty-five minutes ago."

"What did you…hang on, that's from Watchmen!" The Doctor realized

"I didn't know you read it," The Master said

"Yeah! Loved it! Rorschach and Nite Owl!"

The Doctor imitated Rorschach's fighting style, emitting a few 'Hurms'.

"Why do you think I wear this?" The Doctor tapped his overcoat, "found a copy of the comic after I regenerated, had to have the overcoat. I would have worn the mask, but Rose wouldn't let me."

"Remember that time I hit you with a dinner tray?" The Master said, "Where do you think I got the idea?"

"Why do you think I let you do it?"

They realized they had momentarily engaged in comradeship.

"Um, anyway, I'm going to take over the Alliance and use it to rule over the universe, nothing you can do to stop me."

The Master reached to his screwdriver, and turned on of the many dials. Suddenly, he disappeared.

/


	3. Chapter 3

Chapter Three…

/

/

The Master's laugh echoed throughout Serenity, slowly fading away.

"OK, I can fix this," The Doctor said, looking around, "I just need something from my ship."

The Doctor strode across the cargo bay, and attempted to open the TARDIS with his key.

"Rrrg!" The Doctor waved his sonic screwdriver up and down the doors, "Not again! It's been deadlocked from the inside!"

"Is that a problem?" Mal asked

The Doctor thought for a moment.

"No, not this time," The Doctor remembered, "Wash, Jayne, give me a hand?"

The three of them moved the TARDIS forward a few feet. The Doctor walked behind it.

"This time I can get to the back door!"

The Doctor easily slid aside the back door, and stepped into the console room. The cloister bell was ringing, very loudly.

"OK, I can hear you!" The Doctor replied, throwing his overcoat on one of the support columns

/

Mal and Simon walked into the back of the TARDIS.

"Doctor, you have a plan?" Mal asked

"Yeah, but I'll need your help," The Doctor said, "If I can put enough power into the helmic regulator and exert it into a Class Omega black hole, then I might be able to jumpstart time. Simon, hold that lever down!"

Simon did what he said.

"Good. Mal, kick that panel twelve times then ring that bell."

As Mal slammed his leather-and-steel clad feet against the strong coral-like paneling, The Doctor began pulling several levers. The time rotor ascended and descended, whirring and grinding. Finally, it stopped.

"That should have done it. Now…" The Doctor stopped mid-sentence, "Is there a reason you guys are both wearing chains? In fact, I've noticed that everyone on your crew wears one."

"What chains?" Simon asked

The Doctor tugged on the chain Simon wore; it was a dainty silver one, going from his left pocket to his right pocket.

"This chain…" Simon looked at it, "I knew that I had it, but I never noticed it."

Mal pulled on his chain (going from his suspender strap to his pocket), revealing a fob watch with intricate detail on the lid. The Doctor's trademark grin came back on his face.

"_Martha, this watch is me…"_

"_It has been said that the memories of a Time Lord can be stored in a fob watch…"_

"_No, no, no, it's this thing, this device, it re-writes biology. Changes a Time Lord into a human."_

"Oh, brilliant!" he said, gleefully

"What is it?" Mal asked

The Doctor could feel the watch's power; he could hear the extra heartbeat that was contained inside it.

"Nothing…" The Doctor was so happy he almost broke his sonic screwdriver

/

"Did River come in here?" Zoe stuck her head in the TARDIS backdoor

"No, why?" Simon asked

"She's not on the ship."

Simon looked to Mal. Mal looked to The Doctor. The Doctor lunged forward to the TARDIS console.

"Her energy signal disappeared just when The Master did," The Doctor concluded, "The Master has River."

/

With Jayne's held, The Doctor disconnected the TARDIS console from the time rotor and brought it into Serenity's cargo bay. It was still connected to the TARDIS by a long black cord.

"OK, The Master has a limited teleport range," The Doctor explained, "He can only make one long range teleport every week. Captain Reynolds, can you show me a map of the Verse?"

Mal nodded, reached into his pocket, and took out a folded up piece of paper. He tossed it to The Doctor, who opened it up; it expanded out to be three feet wide.

"Mal, what's the scale?" The Doctor asked

Mal told him.

"Oooo…" The Doctor cringed

"What's wrong?" Kaylee asked

"I thought the Alliance was bigger," The Doctor explained, "But judging by this map, he could be on any civilized world."

"Is that a problem?" Simon asked

"No…" The Doctor got back up, and flicked on a console switch, "I've got a backup plan."

/

A small console panel opened up; out of it came a noise like two hearts beating at the same time.

"What's that?" Simon asked

"Shush," The Doctor ordered, "I've got to concentrate."

The heartbeat got louder; The Doctor closed his eyes, and breathed deeply. Then suddenly, his eyes shot open, and he grinned.

"I've got her!" The Doctor said triumphantly, "Right to the last square centimeter!"

The Doctor yanked on a wrist-strap attached to the TARDIS, and eight wrist-straps came out of the bar around the console.

"You might want to hold on," The Doctor advised

/

The TARDIS and the still separated console rocketed through space, bobbing and weaving until it reached its destination, the Pax Research Center on Osiris. It materialized in an operating room. There was a thick metal table in the center of it, with River strapped onto it, apparently unconscious.

"River!" Simon let go of the console, and ran towards her

"Wait!"

The Doctor reached into his pocket, and took out a cricket ball; he hurled it at Simon, knocking him out for the count.

"What did you do that for?" Jayne asked, "Not that I'm complaining."

"Things are never what they seem with The Master," The Doctor explained

/

The seven of them (Simon was still down) crowded around River.

"She's still breathing," Mal said

The Doctor placed his stethoscope on his ears, and listened to River's heartbeat.

"Heartbeat's good," The Doctor noted, "Almost too good. Her heartbeat should be ecstatic, considering her emotions."

The Doctor listened to River's breathing.

"Breathing's too good," The Doctor noted

"Has she always had those scars?" Wash asked

"What scars?" The Doctor asked

Wash pointed to a cut on River's temple, and one on the mirror side of her face. The Doctor touched them, and something shocking happened.

"Look away, look away!" The Doctor ordered

It was too late. The top half of River's head opened up; there was a hissing sound, and the inside of her head was revealed. There was a mass of wires and circuit boards inside, but no brain…


	4. Chapter 4

The seven of them (Simon was still down) crowded around River.

"She's still breathing," Mal said

The Doctor placed his stethoscope on his ears, and listened to River's heartbeat.

"Heartbeat's good," The Doctor noted, "Almost too good."

The Doctor listened to River's breathing.

"Breathing's too good," The Doctor noted

"Has she always had those scars?" Wash asked

"What scars?" The Doctor asked

Wash pointed to a cut on River's temple, and one on the mirror side of her face. The Doctor touched them, and something shocking happened.

"Look away, look away!" The Doctor ordered

It was too late. The top half of River's head opened up; there was a hissing sound, and the inside of her head was revealed. There was a mass of wires and circuit boards inside, but no brain…

/

Inara began to cry. Kaylee threw up, and Wash fainted. Shepherd Book began silently praying. Mal cursed a string of Mandarin offenses. Jayne just stood there.

"That explains a lot," he said

The crew looked up at him, shocked; Mal gave him a look that said 'what is wrong with you?' and 'you horrible man!' at the same time.

"Doctor, is she…" Mal began

"Her brain's been replaced by an electronic one," The Doctor explained, slipping on his glasses, "It keeps her alive, keeps her heart beating."

"Why would anyone do such a thing?" Mal asked

"Brain surgery," The Doctor explained, "it makes it easier to operate on the brain without worrying about the body."

"So The Master took River's brain?"

"Yeah, but that's not the worst of it. Such an operation would require a lot of equipment; this means that The Master has been here a while."

"What's going on?" Simon groaned, waking up

Jayne reached into Kaylee's coveralls, and took out a spanner. He threw it at Simon's head, knocking him out again.

"That's good thinking, the shock of it would have killed him," Book said

"Shock of what?" Jayne asked

"Tell me you saw that coming?" Zoe asked

/

"So, what are we going to do?" Mal asked, "We can't keep throwing spanners at Simon for the rest of his life."

Jayne opened his mouth to object, but a stern glare from Inara stopped him.

"Well, the good thing is, usually when an electric brain is used, it's if the real one is too precious to lose. This one seems to be top of the line, a Huǒ Jù Mù brand."

"So The Master kept her brain?"

"Correctamundo," The Doctor said, "…remind me never to say that again."

The Doctor took out his sonic screwdriver, and used it to close River's head.

"So, how about we go find The Master?" The Doctor asked

Mal and Jayne took out guns.

"Actually, I was thinking of something less violent," The Doctor said, "Doing things the human way."

/

Moments later, the eight of them were back in the TARDIS, watching TV. The Doctor flicked through the channels, looking for the news.

"Doctor, I have some underworld contacts who could do this much faster," Mal said

"It's not that easy," The Doctor explained, "Right now, he could look like any twenty-six people."

"So he's a master of disguise?"

"It's a bit more complicated than that," The Doctor replied, "Let me explain."

The Doctor took out his wallet, and opened it up; nine photos folded out, each of a different person. They were labeled one through nine.

"Is that your family?" Kaylee asked

"Sort of," The Doctor replied, "They're who I used to be. My people have a way of cheating death, but it means we change. Every molecule regenerates, and I become a new man. The Master can do the same."

"So you were this guy?" Zoe grinned, pointing to picture number six

"Yeah," The Doctor nodded, "That was one of my favorite incarnations."

"Really? Why?" Mal asked

The Doctor unfolded the other half of the picture; there was a cute American girl in a pink leotard and shorts.

"That's why," Wash grinned

/

The Professor and The Operative walked proudly into the meeting room. Four old white men, one old Japanese guy, and one middle-aged woman sat at the table, not looking pleased.

"Professor, we gave you a six-month extension, and added seven million credits to your budget," the middle aged woman said, "Either you show us what you have been working on, or we will be forced to cut your funding."

The Professor and The Operative exchanged grins, and nodded.

"Of course, you're entitled to see it," The Professor said, "As you know, the Alliance has trouble controlling the border planets, but we can't stop people from getting away from us. Or can we? What if we created a force that could constantly patrol the edge of space?"

"So you've managed to get our space-mines ready for mass production?" the Japanese man asked

"No, I've managed to create a biological army," The Professor announced, "I had to decimate the planet Miranda quite a few times in order to do so, but a small price to pay."

The Operative held up his sword, and pressed a button on the handle. One of the walls opened, revealing what appeared to be a Plexiglas panel. Behind it stood a terrifying creature. It was human, but clad in torn leather clothes; its face appeared to be torn right off, so was the arm, which was carrying a spiked axe. When the wall opened, the board members had caught the creature in the middle of tearing apart a rather large bear, which impressed them.

"They can fly with unshielded radiation, they are stronger, and they are brutally savage."

"Excellent!" the woman grinned, "I'd like to order ten thousand for the outer rim."

"Now don't decide so quickly," The Professor said, "Perhaps you need a closer look…"

With one hurl of his sword, The Operative smashed the Plexiglas, releasing the creature. The Professor and The Operative were protected by The Professor's perception field, but there was nothing protecting the board members…

/

The Doctor eventually found The Master on the news; he was in the form of Professor Yana, being interviewed about his work with the Ministry of Hate.

"Mal, is that one of those ironic terms?" The Doctor asked, "Like in 1984?"

"Yep," Mal nodded, "The Ministry of Hate actually tries to eliminate hate, among other things. It's sort of a descendant of an old earth organization, Huǒ Jù Mù, ."

"Hurm…" The Doctor waved his screwdriver in front of the screen, rapidly going through the wave cortex, "I see that dumping G-23 Paxilon Hydrochlorate is part of their agenda."

"What does that do?" Mal asked

"We'll have to find out…"

/

Moments later, the Serenity crew was in the TARDIS lab, helping The Doctor with his experiments. The lab was simple, a white room with a large counter of chemicals and oddly enough a police box in the corner.

"Why do you have that there?" Mal asked

"It's a reminder of the lab I used to have a while back, working for UNIT."

"UNIT? That terrorist organization who worked against the noble Chinese government?" Simon asked

The Doctor gave him a withering look.

"You'll have to forgive him, he went to an Alliance-sponsored school," Mal said

"I thought so," The Doctor swished some chemicals together, "Well, there it is."

"Are you going to test it on a lab rat?" Simon asked

"Nope."

The Doctor stuck a beaker underneath a scanner, and it analyzed the chemicals. It displayed the results in Gallifreyan.

"Hm, that's odd," The Doctor said, "Apparently, this would pacify ninety-nine percent of a group, and the other one percent would become feral, wild, evil, almost like…"

The Doctor's eyes widened.

"…Reavers." he completed


	5. Chapter 5

Final part, please review; anything constructive, anything you liked, anything that you didn't understand…

/

/

The TARDIS materialized in the Ministry of Hate office, and the crew piled out. The Ministry of Hate workers were in the middle of a fancy party, celebrating The Professor's accomplishments. Mal fired his gun into the air; the music cut out, everyone's attention was focused on Mal.

"Where's The Professor?" The Doctor demanded

"Right here…"

The crowd split aside to The Master, who wasted no time in taking out his Laser Screwdriver and switching forms to the dark-haired man with the rubbish beard.

"Doctor," he grinned, menacingly

He held up the screwdriver, switching it to laser, when a blast from Mal's gun destroyed it.

"That's OK, my dear Captain," he said, "I have a backup plan…"

The Master swung his arm, and smashed the ice sculpture on the table he was next to; inside it was an electric metal canister.

"The brain of a reader," The Master grinned, "Allows me to control savages."

The Master twisted the container, and hidden doors opened, revealing metal tunnels. The screaming and drumming of Reavers was getting closer.

"The security forces you begged for will now be your downfall," grinned The Master, "Your only chance of being saved from them is by my brain control over them. And you will only get it by the following people stepping down from their positions in the Alliance parliament…"

"That's your plan?" The Doctor was flabbergasted

"Let him talk!" someone yelled, "Our lives depend on it!"

"Oh, please," The Doctor groaned, hopping over a railing, "Allow me."

He placed his hand on his temple, and telekinetically locked the doors.

"How did you figure this out?" growled The Master, "I am The Master, and I…"

"No you're not. The Master I know would never need the brain of a psychic."

The Doctor held up his sonic screwdriver, and The Master was gone. The jar containing River's brain and the laser screwdriver fell to the ground.

"Just a hard-light hologram, controlled by a madman who believes his way is the only right way…"

The Doctor followed the sonic screwdriver's tracker, and spun round to The Operative; everyone gasped.

"It was all for the good of the Alliance!" The Operative said, "I had to do it! For the honor of the Huǒ Jù Mù Institute!"

He lashed his sword at The Doctor, who caught it with the blade of his Swiss Army Knife; with a quick flick of his wrist, he sliced the blade off at the handle.

"You've failed," The Doctor said

"No, I have just been stalled," The Operative replied, "But I'll be back when the Alliance needs me…"

He reached to a button on his sword handle, and teleported away.

/

Four hours later…

/

Simon assisted The Doctor in placing River's brain back in her head. It was a complicated process; the acetylene torch was used just as much as the scalpel. The TARDIS's operating room was well stocked, but a brain transplant was always complicated. The room had the same walls and floor as the console room, but it had stadium chairs and more intense lightning.

"OK, Simon, I've managed to get the basic functions reattached to the skull," The Doctor said, "I can stimulate the synapses so they will grow back, and she'll be back to normal."

Simon wiped the sweat from his brow.

"Doctor, I cannot tell you how thankful I am," he said, "If there's anything I can ever do for you…"

"Oh, it was nothing," The Doctor said, "What I'd really like is to know why The Operative felt the need to use The Master. Or how did he even know about The Master…?"

/

Somewhere in an alliance facility, The Operative sharpened his sword, preparing for his next target, Mal Reynolds. He didn't notice the fob watch in his pocket, nor did he see that it had been slightly pried open, letting it leak gold substance. Anyone listening closely could hear familiar voices…

"_Predictable as ever, Doctor…"_

"_Excellent Doctor, envy is the beginning of all true greatness…"_

"_If The Doctor can be __young__ and __strong__, then so can I!"_

"_Here come the drums!"_

/

Back on Serenity, The Doctor was preparing to leave.

"The thing is," The Doctor said, moving crates away from the TARDIS doors, "You can't open the fob watches. Whatever you're hiding from might still be following you."

"Do you know anything about who we really are?" Simon asked

"Not really," The Doctor replied, "But you'd probably have identities based on your Time Lord names. Mal might have been called 'The Captain'; Inara would be 'The Ambassador'…that kind of stuff."

"So River might be 'The Reader'?" Kaylee guessed

The Doctor stuck his key into the door.

"Actually, River doesn't have a watch," The Doctor replied, "I can't explain it. But I'm sure all will be revealed soon."

The Doctor walked inside the TARDIS.

"I almost forgot, here's your payment," The Doctor said

He tossed Mal a bar of gold bearing the Nazi insignia. Mal looked at it, and was freaked out by the inscription:

_To Doctor,_

_Thanks for introducing me to Jack,_

_Love Addy_

"Anyway, see you around," The Doctor said

The TARDIS door slammed, and he was off…

/

Three months later…

/

Simon sat in his quarters, reading a medical journal. It was his escape from thinking about the deaths of Wash and Shepherd Book, or of his failed marriage to Kaylee. He was interrupted from his deep study by River knocking on the door.

"Come in," he said

The door slid aside, revealing River.

"Hi, 'brother'," she said, smiling

"Hello," Simon replied, suspiciously

"It's been a year," she said

"Since what?"

"Don't you remember? The Time Lord Humanization process, it takes a year to permanently change the exiled Time Lord criminals to complete humans…oh, I forgot."

River walked over to Simon's bed, and picked up his fob watch.

"No!" he exclaimed

The watch flung open; gold and red dust floated through the air, and into Simon's head. He remembered who he was; gone was his formal demeanor, and his grin had returned.

"Magnificent!" he exclaimed, in a posh British accent, "One year as of today, just like I told you to, my faithful companion! Are they transformed?"

River nodded.

"Then let's get going!" Simon said

/

The crew of Serenity heard the pounding footsteps and laughter of Simon and River; Mal stuck his head out of his room, just in time to hear the sound of the TARDIS groaning and wheezing.

"He's back!"

Mal ran down the corridor, being joined by Zoe and Jayne. They ran into the cargo bay where Kaylee and Inara had just arrived.

"Where's the TARDIS?" Inara asked

"Not sure…" Mal looked around, "Where's Simon's cryo-crate? The one he smuggled River in?"

"It was right there," Kaylee said, pointing to an empty space

Mal walked to the spot, and studied it. He then saw that Simon's stethoscope and open fob watch was on the ground.

"Wuh de tyen ah…" Mal said, "I get it now."

"Get what?" Inara asked

"Don't you see it? If my Time Lord name was The Captain, and yours was The Ambassador, then what did that make Simon?"

It hit them like a ton of bricks.

"No!" gasped Kaylee

"You can't be serious!" Zoe exclaimed

"That's impossible!" Inara said

Jayne remained silent.

"Wait, don't tell me, I've almost got it…" he murmured

/

The end


End file.
